Contacts of the helix formed by residues 164 - 185 (chain A) in PDB entry 1Z6Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.8 5.4 - - + -
104A VAL* 3.6 23.1 - - + +
156A CYS* 3.6 32.5 - - - -
161A PHE* 3.1 29.6 + + + +
162A LYS 3.6 10.1 + - - -
163A GLY* 1.3 85.7 - - - +
165A ALA* 1.3 63.7 + - - +
166A LEU 3.4 2.5 - - - -
167A TYR* 3.3 16.3 + + + -
168A CYS* 2.9 28.6 + - - +
203A GLN* 5.9 3.1 - - - -
206A ALA* 3.6 28.9 - - + -
210A SER* 3.1 24.5 + - - -
215A MET* 4.2 17.1 - - + +
219A LEU* 4.1 19.1 - - + -
407A CL 4.4 10.3 - - + -
180B VAL* 4.2 0.7 - - - -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.9 20.0 - - + -
111A LEU* 4.0 14.6 - - + +
163A GLY 3.5 3.6 + - - -
164A TRP* 1.3 75.8 - - - +
166A LEU* 1.3 58.0 + - - +
168A CYS* 4.1 0.7 - - - +
169A ALA* 2.9 32.6 + - - +
177B LEU* 3.6 20.0 - - + +
180B VAL* 3.7 28.3 - - + +
184B GLU* 4.9 2.7 - - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 5.0 2.7 - - - +
102A GLY* 5.2 7.4 - - - -
103A ASP 5.3 4.3 - - - +
111A LEU* 4.1 26.4 - - + +
116A GLN* 4.9 7.0 - - + +
117A VAL* 4.1 15.9 - - + -
120A TYR* 3.3 47.3 - - + -
121A TRP* 3.7 24.5 - - + -
164A TRP 3.4 0.2 - - - -
165A ALA* 1.3 78.8 - - - +
167A TYR* 1.3 59.1 + - - +
169A ALA* 3.9 0.7 - - - +
170A GLY 2.9 24.6 + - - -
129B LEU* 3.6 30.7 - - + -
177B LEU* 4.8 0.2 - - + -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER 3.5 23.6 - - - -
101A LEU* 3.6 33.9 + - + +
104A VAL* 5.5 0.2 - - + -
120A TYR* 3.4 8.4 + - - -
154A SER* 3.8 3.2 - - - -
156A CYS* 3.7 37.5 - - + -
164A TRP* 3.3 17.8 + + + +
166A LEU* 1.3 79.1 - - - +
168A CYS* 1.3 61.6 + - - +
170A GLY* 3.3 1.9 + - - -
171A LYS* 2.9 40.1 + - + +
202A MET* 4.1 11.1 - - - -
407A CL 3.4 23.4 - - + +
801A NAP 2.7 41.1 + - - -
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Residues in contact with CYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A CYS* 3.5 30.3 - - - +
159A GLN 3.6 22.2 - - - -
160A PRO* 4.1 0.4 - - - -
161A PHE* 3.8 17.9 - - - -
164A TRP* 2.9 32.2 + - - +
167A TYR* 1.3 72.2 - - - +
169A ALA* 1.3 58.2 + - - +
171A LYS 3.3 0.7 + - - -
172A ALA* 2.9 31.2 + - - +
176B MET* 3.4 22.4 - - + +
180B VAL* 4.0 6.7 - - + -
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 3.9 15.0 - - + -
165A ALA 2.9 19.0 + - - +
168A CYS* 1.3 76.0 - - - +
170A GLY* 1.3 56.9 - - - +
172A ALA* 3.3 1.7 + - - +
173A ALA* 3.0 29.8 + - - +
173B ALA* 3.5 18.5 - - + +
176B MET* 3.6 12.2 - - - +
177B LEU* 3.6 30.3 - - + +
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Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 4.8 7.4 - - - -
121A TRP* 4.0 9.3 - - - -
124A ASN* 5.4 3.1 - - - -
125A LEU* 3.4 16.0 - - - +
166A LEU 2.9 18.0 + - - -
167A TYR 3.7 0.9 - - - -
169A ALA* 1.3 75.2 - - - +
171A LYS* 1.3 58.0 + - - +
173A ALA 3.3 0.5 + - - -
174A ARG* 2.9 39.6 + - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 5.3 2.8 - - - -
124A ASN* 5.6 1.6 + - - -
152A ILE 2.8 27.5 + - - +
153A SER* 4.2 13.0 - - - -
154A SER* 4.0 13.0 - - - -
156A CYS* 4.2 1.1 - - + -
157A ALA* 3.5 33.2 - - + +
167A TYR* 2.9 39.7 + - + +
168A CYS 3.8 1.1 - - - +
170A GLY* 1.3 73.1 - - - +
172A ALA* 1.3 65.6 + - - +
174A ARG* 3.6 26.6 - - + +
175A ASP* 3.0 21.7 + - - +
801A NAP 3.0 38.4 + - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA* 3.7 24.0 - - - +
168A CYS 2.9 17.4 + - - +
169A ALA 3.8 4.0 - - - +
170A GLY 3.3 0.2 - - - -
171A LYS* 1.3 78.2 - - - +
173A ALA* 1.3 60.3 + - - +
175A ASP* 3.5 3.6 + - - +
176A MET* 3.2 23.0 + - - +
172B ALA* 4.0 18.7 - - + +
176B MET* 4.0 20.6 - - + -
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.5 27.1 - - + -
169A ALA 3.0 17.9 + - - +
172A ALA* 1.3 74.3 - - - +
174A ARG* 1.3 59.3 + - - +
176A MET* 3.1 2.0 + - - -
177A LEU* 2.9 34.1 + - - +
121B TRP* 5.3 0.2 - - + -
169B ALA* 3.6 35.1 - - + +
173B ALA* 4.0 6.9 - - + +
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASN* 3.2 29.1 + - - +
98A ALA 3.9 18.1 + - - -
123A LEU 5.0 0.6 + - - -
124A ASN* 2.8 49.2 + - - +
125A LEU* 3.8 5.8 - - + -
128A MET* 3.5 30.4 - - + +
151A ASN* 2.9 39.9 + - - +
152A ILE 3.6 7.5 + - - -
170A GLY 2.9 23.6 + - - +
171A LYS* 3.6 30.8 - - - +
173A ALA* 1.3 73.9 - - - +
175A ASP* 1.3 65.2 + - - +
177A LEU* 3.3 10.9 + - - +
178A PHE* 3.1 25.8 + - - +
801A NAP 4.5 1.0 + - - -
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASN* 3.0 14.9 + - - -
153A SER* 2.6 26.1 + - - -
157A ALA* 3.7 12.0 - - + +
158A LEU* 4.7 5.0 - - + +
171A LYS 3.0 13.3 + - - +
172A ALA* 3.7 5.2 - - - +
174A ARG* 1.3 75.7 - - - +
176A MET* 1.3 58.3 + - - +
178A PHE 3.4 0.5 + - - -
179A GLN* 2.9 36.0 + - - +
192A ASN* 3.4 24.4 + - - +
252A HIS* 2.8 34.0 + - - +
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Residues in contact with MET 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 3.2 16.1 + - - +
173A ALA 3.1 5.2 + - - +
175A ASP* 1.3 73.5 - - - +
177A LEU* 1.3 66.4 + - - +
179A GLN* 3.2 16.0 + - - +
180A VAL* 3.0 22.6 + - + +
156B CYS 3.8 7.6 - - - +
157B ALA 3.6 23.6 - - - +
158B LEU 3.8 22.7 - - - +
159B GLN 3.9 2.7 - - - +
160B PRO* 3.9 24.7 - - + -
168B CYS* 3.5 40.4 - - + +
169B ALA* 3.7 3.4 - - - +
172B ALA* 4.1 9.0 - - + -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 4.6 9.9 - - + +
128A MET* 4.1 21.5 - - - -
129A LEU* 4.1 36.6 - - + -
173A ALA 2.9 19.8 + - - +
174A ARG* 3.6 9.2 - - - +
176A MET* 1.3 75.4 - - - +
178A PHE* 1.3 63.5 + - + +
180A VAL* 3.1 9.8 + - - +
181A LEU 2.9 23.0 + - - -
108B PHE* 3.5 14.2 - - + -
121B TRP* 4.6 10.5 - - + -
165B ALA* 3.7 34.8 - - + +
166B LEU 4.6 1.3 - - - +
169B ALA* 3.7 10.9 - - + +
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASN* 3.4 23.8 - - - -
128A MET* 3.6 26.0 - - + -
132A THR* 3.5 29.2 - - + -
149A VAL* 3.6 17.3 - - + -
150A VAL 3.7 3.8 - - - -
151A ASN* 3.5 34.3 - - + -
174A ARG 3.1 6.9 + - - +
175A ASP 3.8 0.4 - - - +
177A LEU* 1.3 83.6 - - + +
179A GLN* 1.3 61.4 + - - +
181A LEU* 3.4 9.2 + - + +
182A ALA* 2.9 24.9 + - - +
190A VAL* 3.4 32.9 - - + +
191A LEU 4.1 1.6 - - - -
192A ASN* 3.4 22.4 - - - +
108B PHE* 4.6 4.7 - + - -
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP* 2.9 27.8 + - - +
176A MET* 3.2 28.3 + - - +
178A PHE* 1.3 76.4 - - - +
180A VAL* 1.3 61.4 + - - +
182A ALA* 3.4 8.1 + - - +
183A LEU* 3.3 23.7 + - - +
192A ASN* 4.4 1.9 - - - +
250A GLY* 3.6 23.3 - - - +
158B LEU 5.0 2.3 + - - +
160B PRO* 3.8 31.3 - - + +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A MET* 3.0 19.6 + - - +
177A LEU 3.5 6.5 - - - +
179A GLN* 1.3 73.1 - - - +
181A LEU* 1.3 64.8 - - - +
183A LEU* 3.0 8.8 + - - +
184A GLU* 3.0 40.3 + - + +
108B PHE* 4.8 0.2 - - + -
160B PRO* 4.0 19.5 - - + -
161B PHE 3.6 22.9 - - - +
163B GLY 4.2 0.9 - - - +
165B ALA* 3.8 34.5 - - + +
168B CYS* 4.1 16.4 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A THR* 3.9 11.2 - - + -
136A LEU* 3.8 13.9 - - + -
149A VAL* 3.7 29.8 - - + -
177A LEU 2.9 13.8 + - - +
178A PHE* 3.6 13.2 - - + +
180A VAL* 1.3 77.6 - - - +
182A ALA* 1.3 58.0 + - - +
184A GLU* 4.4 2.7 - - - +
185A GLU* 2.8 55.2 + - + +
188A VAL* 4.9 1.1 - - + -
190A VAL* 4.0 9.0 - - + -
108B PHE* 3.5 46.8 - - + -
109B VAL* 5.2 0.9 - - + -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PHE 2.9 17.0 + - - +
179A GLN 3.6 6.3 - - - +
180A VAL 3.2 0.4 - - - -
181A LEU* 1.3 76.0 - - - +
183A LEU* 1.3 63.1 + - + +
185A GLU 3.9 14.4 - - - +
186A PRO* 4.0 6.8 - - - +
190A VAL* 3.9 11.7 - - + -
249A SER* 3.6 28.9 + - - +
250A GLY* 3.7 20.4 - - - +
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLN 3.3 8.6 + - - +
180A VAL 3.0 9.3 + - - +
182A ALA* 1.3 82.0 - - + +
184A GLU* 1.3 60.5 - - - +
185A GLU 3.7 0.2 + - - -
186A PRO* 4.2 10.6 - - - +
160B PRO* 3.7 41.5 - - + +
161B PHE* 4.3 0.9 - - - -
162B LYS* 3.7 45.2 - - + +
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 3.0 25.8 + - + +
181A LEU* 3.8 5.6 - - - +
183A LEU* 1.3 78.6 - - - +
185A GLU* 1.3 75.3 + - + +
186A PRO* 3.2 10.1 - - - +
107B GLY* 3.3 8.8 - - - -
108B PHE* 2.8 42.5 + - + +
109B VAL 4.7 0.9 + - - -
162B LYS* 4.1 14.1 - - + -
163B GLY* 3.1 35.9 + - - +
165B ALA* 4.9 0.9 - - - +
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 5.3 0.9 - - + -
147A ARG* 3.8 18.9 + - - -
181A LEU* 2.8 33.0 + - + +
182A ALA* 3.9 6.1 - - - +
184A GLU* 1.3 90.1 - - + +
186A PRO* 1.3 62.9 - - - +
187A ASN* 3.1 5.5 + - - +
188A VAL* 2.8 43.3 + - + +
108B PHE* 5.8 0.4 - - + -
109B VAL* 3.7 25.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il